It is my first time doing 16S metagenomic analysis on environmental samples and would appreciate any help on deciding which database I should be using. Silva seems to be the most appropriate database to use for analysis of environmental samples. I am trying to download Silva 138.1 from this link here: https://www.arb-silva.de/download/arb-files/. If you look at the first two options for SSU, you are given the choice of “Ref NR 99” and “Ref”. Which should I use? The website says the Ref NR 99 is the recommended option, but I wanted a second opinion.
Thank you in advance for your help